| Previous changeset 67:19c48f2ec775 (2014-06-17) Next changeset 69:0c4ac210068b (2014-06-18) |
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Commit message:
fix bug in calculations of alignment end |
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modified:
blast2html.py test-data/blast xml example1.html test-data/blast xml example3.html test-data/blast xml example4.html |
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| diff -r 19c48f2ec775 -r fa8a93bdefd7 blast2html.py --- a/blast2html.py Tue Jun 17 18:07:02 2014 +0200 +++ b/blast2html.py Wed Jun 18 12:25:37 2014 +0200 |
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| @@ -83,6 +83,8 @@ @filter def alignment_pre(hsp): + """Create the preformatted alignment blocks""" + step = 60 def split(txt): @@ -99,9 +101,9 @@ offset = 0 for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), step)): yield ( - "Query {:>7} {} {}\n".format(qfrom+offset, qs, qfrom+len(qs)-1) + + "Query {:>7} {} {}\n".format(qfrom+offset, qs, qfrom+offset+len(qs)-1) + " {:7} {}\n".format('', mid) + - "Subject{:>7} {} {}".format(hfrom+offset, hs, hfrom+len(hs)-1) + "Subject{:>7} {} {}".format(hfrom+offset, hs, hfrom+offset+len(hs)-1) ) if qfrom+len(qseq)-1 != qto: |
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| diff -r 19c48f2ec775 -r fa8a93bdefd7 test-data/blast xml example1.html --- a/test-data/blast xml example1.html Tue Jun 17 18:07:02 2014 +0200 +++ b/test-data/blast xml example1.html Wed Jun 18 12:25:37 2014 +0200 |
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| b'@@ -6667,7 +6667,7 @@\n \n <pre class=alignmentgraphic>Query 2 GTCCGTCG 9\n ||||||||\n-Subject 177 GTCCGTCG 170</pre>\n+Subject 177 GTCCGTCG 184</pre>\n </div>\n <div class=hotspot id=hotspot1-26-3>\n <p class=range>\n@@ -6715,7 +6715,7 @@\n \n <pre class=alignmentgraphic>Query 2 GTCCGTC 8\n |||||||\n-Subject 2048 GTCCGTC 2042</pre>\n+Subject 2048 GTCCGTC 2054</pre>\n </div>\n <div class=hotspot id=hotspot1-26-5>\n <p class=range>\n@@ -6853,7 +6853,7 @@\n \n <pre class=alignmentgraphic>Query 8 CGTGAAGA 15\n ||||||||\n-Subject 1634 CGTGAAGA 1627</pre>\n+Subject 1634 CGTGAAGA 1641</pre>\n </div>\n <div class=hotspot id=hotspot1-28-3>\n <p class=range>\n@@ -6994,7 +6994,7 @@\n \n <pre class=alignmentgraphic>Query 8 CGTGAAGA 15\n ||||||||\n-Subject 1634 CGTGAAGA 1627</pre>\n+Subject 1634 CGTGAAGA 1641</pre>\n </div>\n <div class=hotspot id=hotspot1-29-3>\n <p class=range>\n@@ -7111,7 +7111,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 298 TCGTGAAGA 290</pre>\n+Subject 298 TCGTGAAGA 306</pre>\n </div>\n <div class=hotspot id=hotspot1-31-2>\n <p class=range>\n@@ -7672,7 +7672,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-37-2>\n <p class=range>\n@@ -7813,7 +7813,7 @@\n \n <pre class=alignmentgraphic>Query 10 TGAAGAG 16\n |||||||\n-Subject 1569 TGAAGAG 1563</pre>\n+Subject 1569 TGAAGAG 1575</pre>\n </div>\n \n </div>\n@@ -7924,7 +7924,7 @@\n \n <pre class=alignmentgraphic>Query 10 TGAAGAG 16\n |||||||\n-Subject 1569 TGAAGAG 1563</pre>\n+Subject 1569 TGAAGAG 1575</pre>\n </div>\n \n </div>\n@@ -8392,7 +8392,7 @@\n \n <pre class=alignmentgraphic>Query 8 CGTGAAGA 15\n ||||||||\n-Subject 1634 CGTGAAGA 1627</pre>\n+Subject 1634 CGTGAAGA 1641</pre>\n </div>\n <div class=hotspot id=hotspot1-45-3>\n <p class=range>\n@@ -8551,7 +8551,7 @@\n \n <pre class=alignmentgraphic>Query 8 CGTGAAGA 15\n ||||||||\n-Subject 1634 CGTGAAGA 1627</pre>\n+Subject 1634 CGTGAAGA 1641</pre>\n </div>\n <div class=hotspot id=hotspot1-46-3>\n <p class=range>\n@@ -8716,7 +8716,7 @@\n \n <pre class=alignmentgraphic>Query 10 TGAAGAG 16\n |||||||\n-Subject 1569 TGAAGAG 1563</pre>\n+Subject 1569 TGAAGAG 1575</pre>\n </div>\n \n </div>\n@@ -8809,7 +8809,7 @@\n \n <pre class=alignmentgraphic>Query 10 TGAAGAG 16\n |||||||\n-Subject 1569 TGAAGAG 1563</pre>\n+Subject 1569 TGAAGAG 1575</pre>\n </div>\n \n </div>\n@@ -8878,7 +8878,7 @@\n \n <pre class=alignmentgraphic>Query 8 CGTGAAGA 15\n ||||||||\n-Subject 1634 CGTGAAGA 1627</pre>\n+Subject 1634 CGTGAAGA 1641</pre>\n </div>\n <div class=hotspot id=hotspot1-49-3>\n <p class=range>\n@@ -9043,7 +9043,7 @@\n \n <pre class=alignmentgraphic>Query 10 TGAAGAG 16\n |||||||\n-Subject 1569 TGAAGAG 1563</pre>\n+Subject 1569 TGAAGA'..b'y 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-63-2>\n <p class=range>\n@@ -10093,7 +10093,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-64-2>\n <p class=range>\n@@ -10186,7 +10186,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-65-2>\n <p class=range>\n@@ -10279,7 +10279,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-66-2>\n <p class=range>\n@@ -10348,7 +10348,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-67-2>\n <p class=range>\n@@ -10441,7 +10441,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-68-2>\n <p class=range>\n@@ -10534,7 +10534,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-69-2>\n <p class=range>\n@@ -10627,7 +10627,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-70-2>\n <p class=range>\n@@ -10768,7 +10768,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-71-2>\n <p class=range>\n@@ -11263,7 +11263,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-76-2>\n <p class=range>\n@@ -11380,7 +11380,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-77-2>\n <p class=range>\n@@ -11473,7 +11473,7 @@\n \n <pre class=alignmentgraphic>Query 7 TCGTGAAGA 15\n |||||||||\n-Subject 305 TCGTGAAGA 297</pre>\n+Subject 305 TCGTGAAGA 313</pre>\n </div>\n <div class=hotspot id=hotspot1-78-2>\n <p class=range>\n@@ -12961,7 +12961,7 @@\n \n <pre class=alignmentgraphic>Query 5 CGTCGTGA 12\n ||||||||\n-Subject 52 CGTCGTGA 45</pre>\n+Subject 52 CGTCGTGA 59</pre>\n </div>\n \n </div>\n' |
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| diff -r 19c48f2ec775 -r fa8a93bdefd7 test-data/blast xml example3.html --- a/test-data/blast xml example3.html Tue Jun 17 18:07:02 2014 +0200 +++ b/test-data/blast xml example3.html Wed Jun 18 12:25:37 2014 +0200 |
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| @@ -3321,9 +3321,12 @@ </tr> </table> - <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA 74 - ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| |||||||| -Subject 1516 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA 1589</pre> + <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTG 60 + ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | +Subject 1516 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTC 1575</pre> + <pre class=alignmentgraphic>Query 61 TTCGCAGTCCAGAA 74 + ||||| |||||||| +Subject 1576 TTCGCCGTCCAGAA 1589</pre> </div> </div> @@ -3509,9 +3512,12 @@ </tr> </table> - <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA 74 - ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| |||||||| -Subject 2319 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA 2392</pre> + <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTG 60 + ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | +Subject 2319 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTC 2378</pre> + <pre class=alignmentgraphic>Query 61 TTCGCAGTCCAGAA 74 + ||||| |||||||| +Subject 2379 TTCGCCGTCCAGAA 2392</pre> </div> </div> |
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| diff -r 19c48f2ec775 -r fa8a93bdefd7 test-data/blast xml example4.html --- a/test-data/blast xml example4.html Tue Jun 17 18:07:02 2014 +0200 +++ b/test-data/blast xml example4.html Wed Jun 18 12:25:37 2014 +0200 |
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| @@ -1540,9 +1540,12 @@ </tr> </table> - <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA 74 - ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| |||||||| -Subject 2319 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA 2392</pre> + <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTG 60 + ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | +Subject 2319 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTC 2378</pre> + <pre class=alignmentgraphic>Query 61 TTCGCAGTCCAGAA 74 + ||||| |||||||| +Subject 2379 TTCGCCGTCCAGAA 2392</pre> </div> </div> @@ -1585,9 +1588,12 @@ </tr> </table> - <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA 74 - ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| |||||||| -Subject 1516 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA 1589</pre> + <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTG 60 + ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | +Subject 1516 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTC 1575</pre> + <pre class=alignmentgraphic>Query 61 TTCGCAGTCCAGAA 74 + ||||| |||||||| +Subject 1576 TTCGCCGTCCAGAA 1589</pre> </div> </div> |